Groups reads together that appear to have come from the same original molecule, based on the UMI of the read.

$ pbrun umi_fgbio \
--in-fq firstInput.fastq.gz secondInput.fastq.gz \
--ref theReferenceFile.fasta \
--out-dir directoryWithOutput \
--umi-in-header \
--strategy paired
This UMI pipeline is based on Fulcrum Genomics toolkit, processes sequencing reads with molecular barcodes (also known as Unique Molecular Indices, UMIs), which provide impressive error correction and increased accuracy using a sequencing consensus read level.
Input/Output file options
- --in-fq [IN_FQ [IN_FQ ...]]
-
Path to one or more fastq files, each corresponding to a sub-read. Files can be in fastq or fastq.gz format. (default: None)
Option is required.
- --ref REF
-
Path to the reference file (default: None)
Option is required.
- --metadata METADATA
-
Path to a file containing the metadata about the samples. If no file is provided, output reads will be put into unmatched files only. (default: None)
- --out-dir OUT_DIR
-
Path to the directory that will contain all of the generated files. (default: None)
Option is required.
Pipeline Options:
- --umi-in-header
-
Specifies that UMIs are in the read header. (default: False)
- -L INTERVAL, --interval INTERVAL
-
Interval within which to call bqsr from the input reads. All intervals will have a padding of 100 to get read records, and overlapping intervals will be combined. Interval files should be passed using the --interval-file option. This option can be used multiple times (e.g. "-L chr1 -L chr2:10000 -L chr3:20000+ -L chr4:10000-20000") (default: None)
- --bwa-options BWA_OPTIONS
-
Pass supported bwa mem options as one string. The current original bwa mem supported options are -M, -Y, -T (e.g. --bwa-options="-M -Y") (default: None)
- --no-warnings
-
Suppress warning messages about system thread and memory usage. (default: None)
- --read-group-sm READ_GROUP_SM
-
SM tag for read groups in this run. (default: None)
- --read-group-lb READ_GROUP_LB
-
LB tag for read groups in this run. (default: None)
- --read-group-pl READ_GROUP_PL
-
PL tag for read groups in this run. (default: None)
- --read-group-id-prefix READ_GROUP_ID_PREFIX
-
Prefix for the ID and PU tags for read groups in this run. This prefix will be used for all pairs of fastq files in this run. The ID and PU tags will consist of this prefix, and an identifier that will be unique for a pair of fastq files. (default: None)
- -ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING
-
Amount of padding (in base pairs) to add to each interval you are including. (default: None)
- --read-structures [READ_STRUCTURES [READ_STRUCTURES ...]]
-
The read structure for each of the FASTQs. There must be one read structure per input fastq file. (default: None)
- --no-barcode
-
Remove the requirement that input read structures must contain sample barcodes. (default: None)
- --out-metrics OUT_METRICS
-
The file to which per-barcode metrics are written in the output directory. If none given, a file named demux_barcode_metrics.txt will be written to the output directory. If UMIs are in read header, no metrics file will be generated. (default: None)
- --num-zip-threads NUM_ZIP_THREADS
-
Number of CPUs to use for zipping BAM files in a run (default 16 for coordinate sorts and 10 otherwise). (default: None)
- --num-sort-threads NUM_SORT_THREADS
-
Number of CPUs to use for sorting in a run (default 10 for coordinate sorts and 16 otherwise). (default: None)
- --max-records-in-ram MAX_RECORDS_IN_RAM
-
Maximum number of records in RAM when using a queryname or template coordinate sort mode; lowering this number will decrease maximum memory usage. (default: 65000000)
- --strategy STRATEGY
-
The UMI assignment strategy, which can be adjacency or paired. (default: )
Option is required.
- --min-map-q MIN_MAP_Q
-
Minimum mapping quality. (default: 30)
- --num-worker-threads NUM_WORKER_THREADS
-
Number of threads for worker. (default: 14)
- --error-rate-pre-umi ERROR_RATE_PRE_UMI
-
The Phred-scaled error rate for an error prior to the UMIs being integrated. (default: 45)
- --error-rate-post-umi ERROR_RATE_POST_UMI
-
The Phred-scaled error rate for an error post the UMIs have been integrated. (default: 40)
- --min-input-base-quality MIN_INPUT_BASE_QUALITY
-
Ignore bases in raw reads that have Q below this value. (default: 10)
- --min-consensus-base-quality MIN_CONSENSUS_BASE_QUALITY
-
Mask (make ‘N’) consensus bases with quality less than this threshold. (default: 2)
- --min-reads MIN_READS
-
The minimum number of reads to produce a consensus base. (default: 1)
- --out-suffixF OUT_SUFFIXF
-
Output suffix used for paired reads that are first in pair. The suffix must end with ".gz" (default: _1.fastq.gz)
- --out-suffixF2 OUT_SUFFIXF2
-
Output suffix used for paired reads that are second in pair. The suffix must end with ".gz" (default: _2.fastq.gz)
- --out-suffixO OUT_SUFFIXO
-
Output suffix used for orphan/unmatched reads that are first in pair. The suffix must end with ".gz". If no suffix is provided, these reads will be ignored (default: None)
- --out-suffixO2 OUT_SUFFIXO2
-
Output suffix used for orphan/unmatched reads that are second in pair. The suffix must end with ".gz". If no suffix is provided, these reads will be ignored (default: None)
- --out-suffixS OUT_SUFFIXS
-
Output suffix used for single-end/unpaired reads. The suffix must end with ".gz". If no suffix is provided, these reads will be ignored (default: None)
- --rg-tag RG_TAG
-
Split reads into different fastq files based on the read group tag. Must be either PU or ID (default: None)
- --remove-qc-failure
-
Remove reads from the output that have abstract QC failure. (default: None)
- --num-threads NUM_THREADS
-
Number of threads to run. (default: 8)
Common options:
- --logfile LOGFILE
-
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
- --tmp-dir TMP_DIR
-
Full path to the directory where temporary files will be stored.
- --with-petagene-dir WITH_PETAGENE_DIR
-
Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)
- --keep-tmp
-
Do not delete the directory storing temporary files after completion.
- --license-file LICENSE_FILE
-
Path to license file license.bin if not in the installation directory.
- --no-seccomp-override
-
Do not override seccomp options for docker (default: None).
- --version
-
View compatible software versions.
GPU options:
- --num-gpus NUM_GPUS
-
Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.
- --gpu-devices GPU_DEVICES
-
GPU devices to use for a run. By default, all GPU devices will be used. To use specific GPU devices, enter a comma-separated list of GPU device numbers. Possible device numbers can be found by examining the output of the
nvidia-smi
command. For example, using --gpu-devices 0,1 would only use the first two GPUs.